Red Bull and Sebastian Vettel used KERS to power to pole at Sepang on Saturday.
The team did not use the energy-recovery technology when it dominated the Australian GP in Melbourne two weeks ago, but championship leader Vettel said he needed it this time to stave off a resurgent McLaren in Malaysia by just one tenth.
"We came here and solved most of the [reliability] problems," the German said. "I think if we did not have it [KERS] today, we would not be here [on pole]."
So significant has been McLaren's progress in recent weeks that Hamilton, happy to be second best in Australia, was visibly disappointed with his P2 on the Sepang grid.
"These guys [Red Bull] still have a slight edge but it seems we've closed the gap a bit," said the Briton.
Also disappointed was Vettel's teammate and third fastest qualifier Mark Webber, but he said Saturday was a "better performance from me" after a poor showing two weeks ago.
"Mark (P3) had a little KERS alarm that we're looking at," Red Bull boss Christian Horner told the BBC, "but I don't think it was anything significant."
Meanwhile, Vettel said he thinks there will be plenty of pitstops in Sunday's race given the high degradation of the Pirelli tyres.